Target sequence enrichment

Abstract

The present invention provides methods, systems, kits, and compositions for magnetically purifying target nucleic acid sequences from a sample using bait molecules configured to bind both target nucleic acid sequences and magnetic binding particles. In certain embodiments, the bait molecules comprise a short target capture sequence (e.g., 18 to 48 bases), and the methods employ a short hybridization time (e.g., 1-4 hours) and a low hybridization temperature (e.g., about room temperature).

We claim: 
     
         1 . A method of separating target nucleic acid sequences from a target sample comprising:
 a) contacting a target sample with bait molecules to generate a mixed sample,   wherein said target sample comprises a population of target and non-target nucleic acid sequences, and   wherein said bait molecules: i) are free in solution in said mixed sample, and ii) each comprises a ligand and a target capture sequence which is 18 to 48 bases in length;   b) heating said mixed sample to a nucleic acid denaturation temperature;   c) incubating said mixed sample at a hybridization temperature such that said target capture sequences hybridize to said target nucleic acid sequences, wherein said incubating is conducted for no more than 4 hours before performing steps d), e) and f);   d) adding magnetic binding particles to said mixed sample, wherein said magnetic binding particles comprise ligand binding moieties;   e) incubating said mixed sample under conditions such that said bait molecules bind to said magnetic binding particles via said ligands binding to said ligand binding moieties thereby generating a population of target nucleic acid sequence linked magnetic particles; and   f) magnetically separating said target nucleic acid sequence linked magnetic binding particles from said mixed sample thereby generating a population of separated target nucleic acid sequence linked magnetic binding particles.   
     
     
         2 . The method of  claim 1 , wherein said incubating in step c) is conducted for no more than 1.5 hours before performing steps d), e) and f). 
     
     
         3 . The method of  claim 1 , wherein said target capture sequence is 22-35 bases in length. 
     
     
         4 . The method of  claim 1 , wherein said mixed sample, during said incubating in step c), has, or is treated to have, a salt concentration of at least 1.3 M. 
     
     
         5 . The method of  claim 1 , wherein said hybridization temperature in step c) is about 15-30 degrees Celsius. 
     
     
         6 . The method of  claim 1 , wherein said hybridization temperature in step c) is about room temperature. 
     
     
         7 . The method of  claim 1 , further comprising washing said population of separated target nucleic acid sequence linked magnetic particles with a wash solution. 
     
     
         8 . The method of  claim 7 , wherein said washing is conducted at a temperature of about 30-50 degrees Celsius. 
     
     
         9 . The method of  claim 1 , wherein, in step a), said target sample and said bait molecules are further contacted with carrier nucleic acid in order to generate said mixed sample. 
     
     
         10 . The method of  claim 9 , wherein said carrier nucleic acid comprises blocking oligonucleotides and/or human repetitive nucleic acid sequences. 
     
     
         11 . The method of  claim 1 , further comprising contacting said population of separated target nucleic acid sequence linked magnetic binding particles with an aqueous solution at a denaturation temperature, and eluting said target nucleic acid sequences away from said magnetic binding particles to generate a population of eluted target nucleic acid sequences. 
     
     
         12 . The method of  claim 1 , wherein the total amount of nucleic acid in said target sample is between 100 nanograms and 5.0 micrograms. 
     
     
         13 . The method of  claim 1 , wherein said target nucleic acid sequences are pathogenic nucleic acid sequences and said non-target nucleic acid sequences are human nucleic acid sequences. 
     
     
         14 . A method of separating target nucleic acid sequences from a target sample comprising:
 a) contacting a target sample with bait molecules to generate a mixed sample,   wherein said target sample comprises a population of target and non-target nucleic acid sequences, and   wherein said bait molecules: i) are free in solution in said mixed sample, and ii) each comprises a ligand and a target capture sequence which is 23 to 39 bases in length;   b) heating said mixed sample to a nucleic acid denaturation temperature;   c) incubating said mixed sample at about room temperature such that said target capture sequences hybridize to said target nucleic acid sequences, wherein said incubating is conducted for no more than 2 hours before performing steps d), e) and f);   d) adding magnetic binding particles to said mixed sample, wherein said magnetic binding particles comprise ligand binding moieties;   e) incubating said mixed sample under conditions such that said bait molecules bind to said magnetic binding particles via said ligands binding to said ligand binding moieties thereby generating a population of target nucleic acid sequence linked magnetic particles; and   f) magnetically separating said target nucleic acid sequence linked magnetic binding particles from said mixed sample thereby generating a population of separated target nucleic acid sequence linked magnetic binding particles.   
     
     
         15 . The method of  claim 14 , wherein said mixed sample, during said incubating in step c), has, or is treated to have, a salt concentration of at least 1.3 M. 
     
     
         16 . A composition or system comprising:
 a) a solution comprising bait molecules, wherein said bait molecules are free in solution, and wherein said bait molecules comprise a ligand and a target capture sequence 18 to 48 bases in length;   b) magnetic binding particles, wherein said magnetic binding particles comprise ligand binding moieties.   
     
     
         17 . The composition or system of  claim 16 , wherein said target capture sequence is 25-35 bases in length. 
     
     
         18 . The composition or system of  claim 16 , wherein said ligand comprises biotin and said ligand binding moieties comprise streptavidin. 
     
     
         19 . The composition of  claim 16 , wherein said solution has a salt concentration of at least 1.3 M. 
     
     
         20 . The composition of  claim 16 , wherein said solution has a salt concentration of at least 1.9 M.